PhD Chapter 1

Global - Maps and exploration

This series of files compile analyses done for the global analysis of Chapter 1 (version of May 15th).

All analyses have been done with PRIMER-e 6 and R 4.1.2.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

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We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

1. Statistics

Calculation of basic statistics for each variable considered (apart from species densities):

  Mean SD SE Median Min Max 95% CI
depth 22.362 18.426 1.184 18.250 1.000 77.000 2.321
om 1.168 1.072 0.069 0.810 0.168 8.260 0.135
gravel 0.035 0.115 0.007 0.000 0.000 0.809 0.014
sand 0.527 0.360 0.023 0.562 0.000 1.001 0.045
silt 0.273 0.285 0.018 0.152 0.000 0.942 0.036
clay 0.165 0.348 0.022 0.000 0.000 1.000 0.044
  Mean SD SE Median Min Max 95% CI
arsenic 3.559 2.568 0.194 2.700 0.80 21.30 0.380
cadmium 0.133 0.039 0.003 0.130 0.03 0.27 0.006
chromium 57.992 21.914 1.657 54.000 10.90 143.30 3.247
copper 11.205 6.436 0.486 9.900 2.20 32.40 0.953
iron 55387.011 21175.992 1600.755 53398.800 14089.92 188857.22 3137.421
manganese 1148.868 711.475 53.782 959.400 251.67 5962.19 105.412
mercury 0.021 0.025 0.002 0.017 0.00 0.25 0.004
lead 5.030 2.400 0.181 4.900 1.02 12.20 0.356
zinc 57.614 21.047 1.591 52.900 15.90 141.40 3.118
  Mean SD SE Median Min Max 95% CI
S 14.277 6.877 0.534 13.000 1 35.000 1.046
N 225.910 424.411 32.941 74.000 1 2103.000 64.563
H 1.787 0.509 0.039 1.861 0 2.737 0.077
J 0.710 0.173 0.013 0.727 0 1.000 0.026
delta 51.995 13.129 1.019 54.733 0 77.778 1.997
delta_plus 69.141 6.425 0.499 70.152 0 77.778 0.977
delta_star 68.918 9.047 0.702 71.373 0 79.812 1.376
  Mean SD SE Median Min Max 95% CI
S 7.579 4.435 0.312 7.000 0 19.000 0.612
N 39.624 61.123 4.301 24.500 0 674.000 8.429
H 1.417 0.640 0.045 1.482 0 2.646 0.088
J 0.750 0.232 0.016 0.823 0 1.000 0.032
delta 55.227 19.863 1.398 59.778 0 87.500 2.739
delta_plus 76.490 17.269 1.215 80.253 0 87.500 2.381
delta_star 76.147 17.664 1.243 80.398 0 88.001 2.436

2. Maps

2.1. General maps

All stations were not necessarily sampled for every variable characterization:

Habitat

Metals

0.5 mm community

1 mm community

2.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

Depth

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Richness (0.5 mm)

Density (0.5 mm)

Diversity (0.5 mm)

Evenness (0.5 mm)

Distinctness (0.5 mm)

Richness (1 mm)

Density (1 mm)

Diversity (1 mm)

Evenness (1 mm)

Distinctness (1 mm)

3. Figures

3.1. Phylum frequencies

Phylum abundances by community
phylum sp500 sp1000
Annelida 24802 2125
Arthropoda 6532 3066
Mollusca 2899 1765
Nematoda 1377 165
Phoronida 1140 0
Echinodermata 579 828
Cnidaria 86 6
Sipuncula 32 27
Bryozoa 30 0
Nemertea 21 17
Hemichordata 2 0
Chaetognatha 1 0
Brachiopoda 0 2
Platyhelminthes 0 3

3.2. Species estimation curves

0.5 mm community

1 mm community

3.3. Hierarchical Agglomerative Clustering

We used the Ward method for the clustering. To determine the number of clusters, we used multiple methods such as K-means, Elbow or Silhouette.

0.5 mm community

Species densities have been transformed with a (log+1) operation. Three clusters have been determined.

1 mm community

Species densities have been transformed with a (log+1) operation. Stations with 0 or 1 individuals (80, 88 and 130) have been deleted, as they were serious outliers for the plot. Three clusters have been determined.

Habitat

Variables have been standardized by mean and standard-deviation. Three clusters have been determined.

Determination of the number of clusters with several methods
  KL CH Hartigan CCC Scott Marriot TrCovW TraceW Friedman Rubin Cindex DB Silhouette Duda Pseudot2 Beale Ratkowsky Ball Ptbiserial Frey McClain Dunn Hubert SDindex Dindex SDbw
2 0.348 87.96 123 -0.3129 414.1 163701142 53731 1058 348171 1.367 0.3017 1.62 0.3108 0.4783 141.8 4.165 0.3341 529.1 0.364 -0.2151 0.6873 0.0397 0.001 4.156 1.824 1.249
3 4.659 127.5 43.53 5.9 1176 15810870 23337 699.7 727290 2.067 0.2559 1.151 0.4163 0.7095 44.22 1.561 0.3882 233.2 0.552 0.8877 0.8536 0.0422 0.0015 3.401 1.421 0.9941
4 0.9699 114.5 39.56 6.339 1315 15835079 16978 591.9 747758 2.443 0.2341 1.319 0.3753 0.6644 47.98 1.923 0.3736 148 0.5172 0.319 1.287 0.0367 0.0015 3.469 1.263 0.7754
5 0.3773 109.6 85.46 8.768 1529 10227492 13762 507.6 754553 2.849 0.2067 1.233 0.3677 0.4478 59.19 4.647 0.3516 101.5 0.5196 -0.1354 1.563 0.0367 0.0016 3.017 1.143 0.6224
6 2.123 135.8 50.24 18.94 1849 3922592 7501 373 792347 3.876 0.1929 1.008 0.3921 0.5648 56.26 2.925 0.3477 62.17 0.5594 0.3042 1.479 0.0379 0.002 2.865 1.038 0.4619
7 1.609 145 36.34 23.2 2015 2687470 4654 307.6 812181 4.701 0.1624 1.01 0.416 0.4665 37.74 4.27 0.3339 43.94 0.5495 0.2203 1.711 0.0379 0.0021 2.681 0.9332 0.4498
8 1.425 148 28.61 25.6 2127 2209821 3377 266.4 812290 5.429 0.1959 1.007 0.4131 0.4943 44 3.847 0.3188 33.3 0.5485 0.2616 1.75 0.0484 0.0022 2.49 0.8648 0.3749
9 0.6684 148.3 40.7 27.1 2383 969494 2879 237.3 849061 6.092 0.1808 0.9757 0.4274 0.6047 27.46 2.457 0.3041 26.37 0.5431 0.1772 1.815 0.0484 0.0022 2.402 0.8068 0.3446
10 2.595 158.7 20.55 30.56 2567 560685 2031 202.1 860092 7.157 0.1573 0.9431 0.4387 0.404 41.31 5.48 0.2928 20.21 0.5412 0.3612 1.831 0.0484 0.0023 2.253 0.749 0.3775
11 0.477 156.9 37.48 31.24 2630 522523 1623 185.6 862272 7.79 0.15 0.9328 0.4268 1.696 -4.925 -1.458 0.2812 16.87 0.5331 -0.0598 1.88 0.0484 0.0024 2.367 0.7074 0.3243
12 8.916 168.4 9.688 34.49 2775 341016 1219 159.7 862633 9.055 0.1717 0.827 0.4362 0.6722 28.29 1.845 0.2721 13.31 0.5359 1.725 1.853 0.0564 0.0024 2.366 0.6796 0.2497
13 0.1458 161 32.03 33.86 2816 337862 1112 153.2 867543 9.436 0.1641 0.9034 0.3891 0.5433 15.97 3.072 0.2621 11.79 0.479 0.0346 2.341 0.0564 0.0025 4.094 0.656 0.1942
14 3.264 171.1 13.6 36.57 2965 212308 827 134.4 874808 10.76 0.1989 0.9339 0.3974 0.5919 20.68 2.567 0.2544 9.603 0.4823 0.4409 2.272 0.0724 0.0025 4.066 0.6358 0.193
15 1.019 168.6 13.32 36.76 3018 195826 718.8 126.9 876361 11.4 0.1874 0.9609 0.396 0.451 25.57 4.471 0.2465 8.458 0.4665 0.341 2.396 0.0724 0.0025 4.161 0.6108 0.1718

Metals

Variables have been standardized by mean and standard-deviation. Two clusters have been determined.

Determination of the number of clusters with several methods
  KL CH Hartigan CCC Scott Marriot TrCovW TraceW Friedman Rubin Cindex DB Silhouette Duda Pseudot2 Beale Ratkowsky Ball Ptbiserial Frey McClain Dunn Hubert SDindex Dindex SDbw
2 4.327 114 36.77 -2.685 213.4 1.65e+16 10239 944 39.94 1.659 0.2354 1.232 0.3851 0.6987 32.34 2.556 0.4311 472 0.4259 0.1581 0.5802 0.0617 8e-04 2.029 1.869 1.441
3 1.13 86.98 30.74 -3.299 403.7 1.251e+16 9284 778.5 49.88 2.011 0.2243 1.441 0.3188 0.701 40.94 2.535 0.3974 259.5 0.4783 0.2355 0.7284 0.0663 0.0012 2.434 1.703 1.204
4 3.334 78.14 14.58 -2.483 595.3 7.444e+15 5946 660.5 55.93 2.371 0.1892 1.434 0.3406 0.6838 37 2.743 0.3748 165.1 0.5184 3.424 0.9056 0.0663 0.0013 2.366 1.583 1.038
5 1.054 66.86 12.71 -3.035 667 7.721e+15 5413 608.6 60.54 2.573 0.1818 1.414 0.2377 0.7734 14.94 1.725 0.3456 121.7 0.4324 0.7738 1.468 0.0418 0.0014 2.72 1.489 1.077
6 0.3482 59.67 23.64 -3.385 741.5 7.263e+15 5003 566.3 63.44 2.765 0.1817 1.56 0.1993 0.6471 12 3.133 0.324 94.38 0.4056 -0.0512 1.844 0.0446 0.0015 2.703 1.412 0.836
7 3.966 60.26 9.604 -1.462 935.8 3.258e+15 3941 496.8 71 3.152 0.1686 1.498 0.2216 0.6456 30.19 3.237 0.3102 70.97 0.4231 1.721 1.804 0.0446 0.0016 2.764 1.343 0.8493
8 0.2883 55.64 21.61 -1.329 1005 2.868e+15 3674 469.9 74.03 3.332 0.162 1.509 0.2139 0.5388 20.55 4.935 0.294 58.74 0.3715 -0.0064 2.473 0.0446 0.0017 3.131 1.28 0.6832
9 1.098 57.34 21 1.181 1133 1.744e+15 2600 416.1 76.29 3.764 0.1897 1.328 0.2213 0.5854 9.917 3.97 0.285 46.23 0.3833 -0.0608 2.418 0.0566 0.0017 3.161 1.231 0.7533
10 1.15 59.39 19.66 3.634 1375 5.395e+14 2077 369.4 85.89 4.24 0.1825 1.255 0.2353 0.2913 14.6 12.52 0.2761 36.94 0.3903 -0.037 2.362 0.0566 0.0018 3.054 1.178 0.6423
11 0.8698 61.41 23.87 5.892 1564 2.216e+14 1611 330 95.33 4.745 0.1791 1.17 0.2487 1.495 -0.9929 -1.49 0.2674 30 0.3932 -0.0856 2.339 0.0566 0.0018 2.776 1.121 0.532
12 1.306 65.72 20.27 8.912 1737 9.806e+13 1322 288.1 101.4 5.435 0.1872 1.059 0.2654 0.5018 11.91 5.502 0.2605 24.01 0.3949 0.023 2.325 0.0597 0.0019 2.465 1.069 0.3011
13 1.94 69 12.07 11.34 1863 5.623e+13 942.1 256.3 107.5 6.111 0.1804 1.03 0.2768 0.2741 39.72 14.91 0.2535 19.71 0.3987 0.1664 2.3 0.0597 0.0019 2.447 1.032 0.287
14 0.3842 68.94 30.93 12.35 1961 3.722e+13 782.8 238.5 112 6.566 0.1759 0.9842 0.2656 0.8986 1.58 0.6324 0.246 17.03 0.3982 -0.0703 2.317 0.0597 0.0019 2.561 0.9877 0.2443
15 2.956 78.03 12.46 16.6 2129 1.632e+13 546.8 200.1 122.7 7.828 0.3138 0.904 0.2788 0.6027 15.16 3.794 0.2411 13.34 0.4036 0.3758 2.263 0.1098 0.002 2.3 0.9477 0.2017

3.4. Principal Component Analysis

Habitat

Variables have been standardized by mean and standard-deviation.

Metals

Variables have been standardized by mean and standard-deviation.

3.5. Non-metric Multidimensional Scaling

0.5 mm community

Species densities have been transformed with a (log+1) operation.

1 mm community

Species densities have been transformed with a (log+1) operation. Stations with 0 or 1 individuals (80, 88 and 130) have been deleted, as they were serious outliers for the plot.

Habitat

Variables have been standardized by mean and standard-deviation.

Metals

Variables have been standardized by mean and standard-deviation.

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